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Deep Learning Solution for Quantification of Fluorescence Particles on a Membrane
No full textThe detection and quantification of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus particles in ambient waters using a membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) method can play an important role in large-scale environmental surveillance for early warning of potential outbreaks. However, counting particles or cells in fluorescence microscopy is an expensive, time-consuming, and tedious task that only highly trained technicians and researchers can perform. Although such objects are generally easy to identify, manually annotating cells is occasionally prone to fatigue errors and arbitrariness due to the operator’s interpretation of borderline cases. In this research, we proposed a method to detect and quantify multiscale and shape variant SARS-CoV-2 fluorescent cells generated using a portable (mgLAMP) system and captured using a smartphone camera. The proposed method is based on the YOLOv5 algorithm, which uses CSPnet as its backbone. CSPnet is a recently proposed convolutional neural network (CNN) that duplicates gradient information within the network using a combination of Dense nets and ResNet blocks, and bottleneck convolution layers to reduce computation while at the same time maintaining high accuracy. In addition, we apply the test time augmentation (TTA) algorithm in conjunction with YOLO’s one-stage multihead detection heads to detect all cells of varying sizes and shapes. We evaluated the model using a private dataset provided by the Linde + Robinson Laboratory, California Institute of Technology, United States. The model achieved a [email protected] score of 90.3 in the YOLOv5-s6
Periodicity-Aware Signal Denoising Using Capon-Optimized Ramanujan Filter Banks and Pruned Ramanujan Dictionaries
No full textWe propose a ‘periodicity-aware’ hybrid analysis-synthesis framework for denoising discrete-time periodic signals. Our method uses Ramanujan filter banks (RFB) for analysis and dictionaries for synthesis. The synthesis dictionary retains appropriate subspaces for signal reconstruction, by pruning the Ramanujan dictionary based on the outputs of the RFB. Unlike the other existing denoising methods, a unique advantage of the proposed method is that the denoised output is guaranteed to be composed of integer-periodic components with periods smaller than a pre-selected value. Our method works well even when the signal length is small, and has a high SNR gain over a wide range of input signal SNRs. Furthermore, we propose to adapt each filter in the analysis bank to the incoming data, by optimizing the filter coefficients through a multi-band Capon formulation. This helps in suppressing the spurious energy peaks generated from higher period filters in the analysis bank, further improving the denoising performance. Implementing multiband Capon filters requires inverses of several autocorrelation matrices. To reduce computations, a way to recursively compute these inverses based on Levinson's recursion is discussed. Next, we prove several multirate properties of Ramanujan subspace signals. An important property among these is that after decimation, a q -th Ramanujan subspace signal still remains in the q -th Ramanujan space, if and only if the decimation rate M is coprime to q. This is helpful to further reduce computations required in the analysis part of the denoising framework by downsampling the filter outputs. Extensive Monte-Carlo simulations comparing different variants of the proposed method and several existing denoising methods are also provided
Hazard Potential in Southern Pakistan: A Study on the Subsidence and Neotectonics of Karachi and Surrounding Areas
No full textCoastal communities in deltaic regions worldwide are subject to subsidence through a combination of natural and anthropogenic processes. The city of Karachi in southern Pakistan is situated along the diffuse western boundary of the tectonically active Indian Plate, making it more susceptible to natural subsidence processes from plate motion-related deformational events such as earthquakes and faulting. Karachi has a dense population of over 16 million people, and determining the rate of subsidence and extent of neotectonic activity is crucial for mitigating seismic hazards. Excessive abstraction of groundwater and extensive groundwater use in irrigation are some of the anthropogenic contributions to subsidence in the area. A combination of the lack of historical data and few previous studies of the area make it difficult to determine the rate and extent of deformation in this region. We present an analysis of subsidence and neotectonic activity in Karachi and its surrounding areas using Interferometric Synthetic Aperture Radar (InSAR) timeseries techniques. The InSAR results for satellite LOS velocity change in both ascending and descending Sentinel-1 tracks indicate subsidence in key residential and industrial areas. Further decomposition into two dimensions (east–west and vertical) quantifies subsidence in these areas up to 1.7 cm per year. Furthermore, InSAR data suggest the presence of an active north–east dipping listric normal fault in North Karachi that is confirmed in the shallow subsurface by a 2D seismic line. Subsidence is known to cause the reactivation of faults, which increases the risk of damage to infrastructure
General relativistic stream crossing in tidal disruption events
No full textA star is tidally stretched into an elongated stream after being disrupted by a supermassive black hole (BH). Using an approximate tidal equation, we calculate the stream’s thickness evolution along its geodesic, during which we treat the effect of nozzle shocks as a perfect bounce. Self-intersection occurs when the closest approach separation is smaller than the stream thickness. We explore a wide parameter space of orbital angular momenta, inclinations, and BH spins to obtain the properties of stream intersection. Two collision modes are identified: in ∼half of the cases, the collision occurs near the pericentre at an angle close to 0o (‘rear-end’ mode) and the other half have collisions far from the pericentre with collision angles close to 180o (‘head-on’ mode). The intersection typically occurs between consecutive half-orbits with a delay time that spans a wide range (from months up to a decade). The intersection radius generally increases with the orbital angular momentum and depends less strongly on the inclination and BH spin. The thickness ratio of the two colliding ends is of order unity and the transverse separation is a small fraction of the sum of the two thicknesses, so a large fraction of the stream’s mass is shock heated in an offset collision. Many of the numerical results can be analytically understood in a post-Newtonian picture, where we find the reason for stream collision to be a geometric one. Future hydrodynamic simulations including recombination are needed to understand the long-term effects of pressure forces which are neglected here
The Meaning of Pressure for Primary Magmas: New Insights From PRIMELT3‐P
No full textThis paper reports new software, PRIMELT3-P, for computing the pressure and temperature range over which a primary basaltic magma was formed by adiabatic decompression and fractional melting of fertile mantle peridotite. The underlying model was developed to explore the meaning of magmatic pressure and its connection to the physics of mantle melting, melt extraction, and melt migration. We present a comparison of the results of the batch melting model FractionatePT3 (Lee et al., 2009, https://doi.org/10.1016/j.epsl.2008.12.020) and the new fractional melting model PRIMELT3-P, each applied to basalts from various localities, with a particular focus on Hawai'i and Iceland. The unexpected result is that pressures for batch melting and fractional melting are quite similar across a broad range of potential temperatures, agreeing to within ±0.29 GPa (1σ) when applied to magmas that pass tests for derivation from peridotite sources. Although samples from both Hawai'i and Iceland yield a range of final pressures of melting, the minimum final pressure in each location coincides with independent geophysical constraints—the depth to the lithosphere-asthenosphere boundary beneath Hawai'i and to the Moho below Iceland. These results clarify the meaning of primary magma pressure, but the concept remains complex. We suggest that computed temperature and pressure arrays arising from heterogeneous peridotite-source primary magmas may reflect melt transport and mixing in a thermally zoned mantle plume with a complex network of branching melt channels that nucleate over a range of depths
Exploring supermassive black hole physics and galaxy quenching across halo mass in FIRE cosmological zoom simulations
No full textFeedback from accreting supermassive black holes (SMBHs) is thought to be a primary driver of quenching in massive galaxies, but how to best implement SMBH physics into galaxy formation simulations remains ambiguous. As part of the Feedback in Realistic Environments (FIRE) project, we explore the effects of different modelling choices for SMBH accretion and feedback in a suite of ∼500 cosmological zoom-in simulations across a wide range of halo mass (10¹⁰–10¹³ M_⊙). Within the suite, we vary the numerical schemes for BH accretion and feedback, accretion efficiency, and the strength of mechanical, radiative, and cosmic ray feedback independently. We then compare the outcomes to observed galaxy scaling relations. We find several models satisfying observational constraints for which the energetics in different feedback channels are physically plausible. Interestingly, cosmic rays accelerated by SMBHs play an important role in many plausible models. However, it is non-trivial to reproduce scaling relations across halo mass, and many model variations produce qualitatively incorrect results regardless of parameter choices. The growth of stellar and BH mass are closely related: for example, overmassive BHs tend to overquench galaxies. BH mass is most strongly affected by the choice of accretion efficiency in high-mass haloes, but by feedback efficiency in low-mass haloes. The amount of star formation suppression by SMBH feedback in low-mass haloes is determined primarily by the time-integrated feedback energy. For massive galaxies, the ‘responsiveness’ of a model (how quickly and powerfully the BH responds to gas available for accretion) is an additional important factor for quenching
Self-organization principles in stem-cell-derived synthetic embryo models
No full textAs embryos, we were extremely lucky to survive implantation, when we transitioned from a simple ball of undifferentiated cells to a complex structure of distinct lineages. During development, fertilization generates a totipotent zygote that ultimately gives rise to the myriad cell types of the whole organism. In mouse embryos, the first cell fate decision leads to trophectoderm (TE) progenitors on the outside of the early embryo, surrounding the inner cell mass. Epiblast (EPI) and primitive endoderm (PE) cells then arise from the inner cell mass and are initially intermingled (embryonic day 3.5). Thus, the mammalian pre-implantation embryo comprises three lineage compartments: TE, destined to become the placenta; PE, destined to become the yolk sac; and EPI, pluripotent cells that will generate the entire body.
Just before mouse embryo implantation, PE cells sort “below” the EPI, and the TE organizes into two regions. The polar TE forms “above” the EPI and will become extra-embryonic ectoderm (ExE), whereas mural TE surrounds the blastocyst cavity and will invade the uterus. After implantation, the ExE and EPI become enveloped by the PE-derived visceral endoderm, forming the “egg cylinder” (Figure 1A). These dramatic reorganization and transition events are essential for life and viability but are frequently unsuccessful, and how they occur has remained a mystery. Although the self-assembly instructions are intrinsic to the embryo, they have been impossible to uncover—because during this process, the embryo is embedded within the mother and, hence, is inaccessible
Hidden depths in the local Universe: The Stellar Stream Legacy Survey
No full textContext. Mergers and tidal interactions between massive galaxies and their dwarf satellites are a fundamental prediction of the Lambda-cold dark matter cosmology. These events are thought to provide important observational diagnostics of non-linear structure formation. Stellar streams in the Milky Way and Andromeda are spectacular evidence for ongoing satellite disruption. However, constructing a statistically meaningful sample of tidal streams beyond the Local Group has proven a daunting observational challenge, and the full potential for deepening our understanding of galaxy assembly using stellar streams has yet to be realised.
Aims. Here we introduce the Stellar Stream Legacy Survey, a systematic imaging survey of tidal features associated with dwarf galaxy accretion around a sample of ∼3100 nearby galaxies within z ∼ 0.02, including about 940 Milky Way analogues.
Methods. Our survey exploits public deep imaging data from the DESI Legacy Imaging Surveys, which reach surface brightness as faint as ∼29 mag arcsec⁻² in the r band. As a proof of concept of our survey, we report the detection and broad-band photometry of 24 new stellar streams in the local Universe.
Results. We discuss how these observations can yield new constraints on galaxy formation theory through comparison to mock observations from cosmological galaxy simulations. These tests will probe the present-day mass assembly rate of galaxies, the stellar populations and orbits of satellites, the growth of stellar halos, and the resilience of stellar disks to satellite bombardment
Mapping frontoinsular cortex from diffusion microstructure
No full textWe developed a novel method for mapping the location, surface area, thickness, and volume of frontoinsular cortex (FI) using structural and diffusion magnetic resonance imaging. FI lies in the ventral part of anterior insular cortex and is characterized by its distinctive population von Economo neurons (VENs). Functional neuroimaging studies have revealed its involvement in affective processing, and histopathology has implicated VEN loss in behavioral-variant frontotemporal dementia and chronic alcoholism; however, structural neuroimaging of FI has been relatively limited. We delineated FI by jointly modeling cortical surface geometry and its coincident diffusion microstructure parameters. We found that neurite orientation dispersion in cortical gray matter can be used to map FI in specific individuals, and the derived measures reflect a range of behavioral factors in young adults from the Human Connectome Project (N=1052). FI volume was larger in the left hemisphere than the right (31%), and the percentage volume of FI was larger in women than men (15.3%). FI volume was associated with measures of decision-making (delay discounting, substance abuse), emotion (negative intrusive thinking and perception of hostility), and social behavior (theory of mind and working memory for faces). The common denominator is that larger FI size is related to greater self-control and social awareness
Gut microbiota suppress feeding induced by palatable foods
No full textFeeding behaviors depend on intrinsic and extrinsic factors including genetics, food palatability, and the environment. The gut microbiota is a major environmental contributor to host physiology and impacts feeding behavior. Here, we explored the hypothesis that gut bacteria influence behavioral responses to palatable foods and reveal that antibiotic depletion (ABX) of the gut microbiota in mice results in overconsumption of several palatable foods with conserved effects on feeding dynamics. Gut microbiota restoration via fecal transplant into ABX mice is sufficient to rescue overconsumption of high-sucrose pellets. Operant conditioning tests found that ABX mice exhibit intensified motivation to pursue high-sucrose rewards. Accordingly, neuronal activity in mesolimbic brain regions, which have been linked with motivation and reward-seeking behavior, was elevated in ABX mice after consumption of high-sucrose pellets. Differential antibiotic treatment and functional microbiota transplants identified specific gut bacterial taxa from the family S24-7 and the genus Lactobacillus whose abundances associate with suppression of high-sucrose pellet consumption. Indeed, colonization of mice with S24-7 and Lactobacillus johnsonii was sufficient to reduce overconsumption of high-sucrose pellets in an antibiotic-induced model of binge eating. These results demonstrate that extrinsic influences from the gut microbiota can suppress the behavioral response toward palatable foods in mice